Little is known of his early life, but it is believed that he was born in Oxford, England around 1550 into a devoutly Catholic family and grew up during the Penal Laws. He became a carpenter presumably by trade, and for about twenty years, built hiding-places for priests in the homes of Catholic families. He frequently travelled from one house to another, under the name of "Little John", accepting only the necessities of life as payment before starting off for a new project.[2]

Owen was only slightly taller than a dwarf, and suffered from a hernia. Nevertheless, his work often involved breaking through thick stonework; and to minimize the likelihood of betrayal he often worked at night, and always alone. The number of hiding-places he constructed will likely never be known. Due to the ingenuity of his craftsmanship, some may still be undiscovered.[3]

For many years, Owen worked in the service of the Jesuit priest Henry Garnet, and was admitted into the Society of Jesus as a lay brother. He was first arrested in 1582 or 1583, after the execution of Edmund Campion, for publicly proclaiming that martyr's innocence, but was later released. He was arrested again in 1594, and was tortured, but revealed nothing. He was released after a wealthy Catholic family paid a fine on his behalf; the jailers believing that he was merely the insignificant friend of some priests. He resumed his work, and is believed to have masterminded the escape of Jesuit Father John Gerard's from the Tower of London in 1597.

Early in 1606, Owen was arrested a final time at Hindlip Hall in Worcestershire,[4] giving himself up voluntarily in hope of distracting attention from some priests who were hiding nearby. Realizing just whom they had caught and his value, Robert Cecil exulted: "It is incredible, how great was the joy caused by his arrest... knowing the great skill of Owen in constructing hiding places, and the innumerable quantity of dark holes which he had schemed for hiding priests all through England."[1]

After being committed to the Marshalsea, Owen was then removed to the Tower. Under English law, he was presumably exempt from torture, having been maimed a few years before when a horse had fallen on him. Nonetheless, he was submitted to terrible "examinations" on the Topcliffe rack, dangling from a wall with both wrists held fast in iron gauntlets and his body hanging. When this proved insufficient to make him talk, heavy weights were added to his feet.

The exact date of his death in 1606 is not agreed. Most sources cite 2 March, while others place his death on 12 November. Father Gerard wrote of him:

“

"I verily think no man can be said to have done more good of all those who laboured in the English vineyard. He was the immediate occasion of saving the lives of many hundreds of persons, both ecclesiastical and secular."